Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate 15367 b1247 oligopeptide transporter subunit (NCBI)
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Keio:15367 Length = 334 Score = 185 bits (469), Expect = 2e-51 Identities = 115/322 (35%), Positives = 184/322 (57%), Gaps = 23/322 (7%) Query: 2 KEILLKAENVRAYYKLEK---------VSVKAVDGLSFEILEDEVIGVVGESGCGKTTLS 52 +++LL+ +++ +++++ ++KAVDG++ + E E +GVVGESGCGK+T + Sbjct: 8 RKVLLEIADLKVHFEIKDGKQWFWQPPKTLKAVDGVTLRLYEGETLGVVGESGCGKSTFA 67 Query: 53 NVIFMNMVKPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPT 112 I + +VK DG + EL M DE + +I +I Q + +L P Sbjct: 68 RAI-IGLVKA---TDGHVAWLGK----ELLGMKPDEWRAV--RSDIQMIFQDPLASLNPR 117 Query: 113 IRMEKYVRHLAESHG--IDEEELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAI 170 + + + + ++ + +E+ ++ + +VGL P I RYP E SGG QR IA Sbjct: 118 MTIGEIIAEPLRTYHPKMSRQEVRERVKAMMLKVGLLPNLINRYPHEFSGGQCQRIGIAR 177 Query: 171 ATILNPSLLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMI 230 A IL P L+I DEP SALDV Q ++ +L Q++R+ + S+IFI HD+A V+ I+DR++ Sbjct: 178 ALILEPKLIICDEPVSALDVSIQAQVVNLLQQLQRE-MGLSLIFIAHDLAVVKHISDRVL 236 Query: 231 IMYAGKIVEFAPVESLLEKPLHPYTQGLFNSVLTPEPEVKK-RGITTIPGAPPNLINPPS 289 +MY G VE + + PLHPYT+ L ++V P+P+++K + I + G P+ INPPS Sbjct: 237 VMYLGHAVELGTYDEVYHNPLHPYTRALMSAVPIPDPDLEKNKTIQLLEGELPSPINPPS 296 Query: 290 GCRFHPRCPHAMDVCKEKEPPL 311 GC F RCP A C + P L Sbjct: 297 GCVFRTRCPIAGPECAKTRPVL 318 Lambda K H 0.321 0.138 0.405 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 302 Number of extensions: 12 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 330 Length of database: 334 Length adjustment: 28 Effective length of query: 302 Effective length of database: 306 Effective search space: 92412 Effective search space used: 92412 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory